useful protein tools

A list of useful webservers and tools that are relatively easy to use for protein analysis

1. Seamdock - super easy web server docking https://bioserv.rpbs.univ-paris-diderot.fr/services/SeamDock/

2. CABS-flex2 - protein flexibility easily from PDB structures https://biocomp.chem.uw.edu.pl/CABSflex2

3. pubchem sketcher for chemical structures https://pubchem.ncbi.nlm.nih.gov//edit3/index.html

4. Robetta fold - super easy protein structure prediction but not as good as alphafold for monomers https://robetta.bakerlab.org/

5. Expasy plot param - gives lots of useful basic info about your protein e.g. MW, size, isoelectric point, amino acid composition, stability index etc…. https://web.expasy.org/cgi-bin/protparam/protparam

6. Web server ramachandran plot easy to use displays allowed/disallowed regions good as a sanity check for structures https://swift.cmbi.umcn.nl/servers/html/ramaplot.html

7. Random sequence generator https://www.bioinformatics.org/sms2/random_protein.html

8. Toxinpred2 - protein toxicity predictor https://webs.iiitd.edu.in/raghava/toxinpred2/

9. RCSB PDB 3D view - easy protein structure viewer. Easier but with less options than Pymol. https://www.rcsb.org/3d-view

10. Kdeep - binding affinity prediction tool. https://playmolecule.org/Kdeep/